Merge pull request #19 from nlmixr2/cran-fixes

Cran fixes

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rxode2random
 Title: Random Number Generation Functions for 'rxode2'
-Version: 2.0.11.9001
+Version: 2.0.12
 Authors@R: c(
     person("Matthew L.", "Fidler", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8538-6691")),
@@ -22,12 +22,12 @@ Imports:
     Rcpp,
     checkmate,
     lotri,
-    rxode2parse (> 2.0.13)
+    rxode2parse (>= 2.0.17)
 Suggests:
     testthat (>= 3.0.0)
 LinkingTo:
     sitmo,
-    rxode2parse (>= 2.0.12),
+    rxode2parse (>= 2.0.17),
     Rcpp,
     RcppArmadillo,
     BH

NEWS.md

@@ -1,4 +1,4 @@
-# rxode2random (development version)
+# rxode2random 2.0.12
 
 - Added function `dfWishart` which gives (by simulation) an
   approximation of the degrees of freedom of a Wishart to match a
@@ -7,6 +7,9 @@
 - Added function `swapMatListWithCube` which swaps omegaList with
   omegaCube values
 
+- Ensure that the outputs are integers (instead of long integers) as
+  requested by CRAN for some checking functions.
+
 # rxode2random 2.0.11
 
 - Fix qassert LTO

R/dfWishart.R

@@ -61,7 +61,7 @@ dfWishart <- function(omega, n, rse, upper, totN=1000, diag=TRUE, seed=1234) {
   .lower <- .d[1] + 3.1
   .upper <-  upper
   rxWithSeed(seed, {
-    uniroot(dfWishartCalcRse, lower=.lower, upper=.upper, omega=omega, totN=totN, rse=rse, diag=diag)
+    stats::uniroot(dfWishartCalcRse, lower=.lower, upper=.upper, omega=omega, totN=totN, rse=rse, diag=diag)
   })
 }
 #' Swaps the matrix list with a cube

R/rxrandom.R

@@ -9,7 +9,7 @@
 #' `rxnorm` simulates using the threefry sitmo generator;
 #'
 #' @return normal random number deviates
-#' 
+#'
 #' @importFrom Rcpp sourceCpp
 #' @importFrom stats setNames
 #' @useDynLib rxode2random, .registration=TRUE
@@ -69,7 +69,7 @@ rxpois <- function(lambda, n = 1L, ncores = 1L) {
 #' rxt(df = 3, n = 10, ncores = 2) # You can parallelize the simulation using openMP
 #'
 #' rxt(4) ## The first argument is the df parameter
-#' 
+#'
 #' @export
 rxt <- function(df, n = 1L, ncores = 1L) {
   checkmate::assertNumeric(df, len = 1, lower = 0)
@@ -94,7 +94,7 @@ rxt <- function(df, n = 1L, ncores = 1L) {
 #' rxunif(min = 0, max = 4, n = 10, ncores = 2) # You can parallelize the simulation using openMP
 #'
 #' rxunif()
-#' 
+#'
 #' @export
 rxunif <- function(min = 0, max = 1, n = 1L, ncores = 1L) {
   checkmate::assertNumeric(min, len = 1)
@@ -708,10 +708,10 @@ rxRmvn <- function(n, mu = NULL, sigma, lower = -Inf, upper = Inf, ncores = 1, i
 #'     `omega` matrix of standard deviations
 #'
 #' @param omegaIsChol is an indicator of if the omega matrix is in
-#'   the Cholesky decomposition. This is only used when code{type="invWishart"}
+#'   the Cholesky decomposition. This is only used when \code{type="invWishart"}
 #'
 #' @param returnChol Return the Cholesky decomposition of the
-#'   covariance matrix sample. This is only used when code{type="invWishart"}
+#'   covariance matrix sample. This is only used when \code{type="invWishart"}
 #'
 #' @param diagXformType Diagonal transformation type.  These could be:
 #'
@@ -1039,11 +1039,11 @@ rxWithPreserveSeed <- function(code) {
 #'
 #' @return md5 hash of rxode2random revision
 #' @author Matthew L. Fidler
-#' @export 
+#' @export
 #' @examples
 #' rxode2randomMd5()
 rxode2randomMd5 <- function() {
-  rxode2random.md5  
+  rxode2random.md5
 }
 
 
@@ -1072,13 +1072,13 @@ rxode2randomMd5 <- function() {
 
 #' Expand parameters
 #'
-#'  
+#'
 #' @param object rxode2 model variables object
 #' @param params parameters to expand
 #' @param events event table to help with the expansion
 #' @param control control structure to help with the parameter generation
 #' @return Expanded parameters for simulation
-#' @export 
+#' @export
 #' @author Matthew L. Fidler
 #' @keywords internal
 .expandPars <- function(object, params, events, control) {

R/zzzz.R

@@ -0,0 +1,12 @@
+.rxode2parseVersion <- utils::packageVersion("rxode2parse")
+.onLoad <- function(libname, pkgname) {
+  if (!identical(.rxode2parseVersion, utils::packageVersion("rxode2parse"))) {
+    stop("rxode2 compiled with rxode2parse '", as.character(.rxode2parseVersion),
+         "' but rxode2parse '", as.character(utils::packageVersion("rxode2parse")),
+         "' is loaded\nRecompile rxode2 with the this version of rxode2parse",
+         call. = FALSE
+         )
+  } else {
+    requireNamespace("rxode2parse", quietly=TRUE)
+  }
+}

src/checkmate_stub.c

@@ -41,28 +41,28 @@ void qstrict0(SEXP nn, const char *what){
   R_xlen_t pos = find_missing_string(nn);
   if (pos > 0) {
     UNPROTECT(1);
-    Rf_errorcall(R_NilValue, "Must have %s, but is NA at position %i", what, pos);
+    Rf_errorcall(R_NilValue, "Must have %s, but is NA at position %i", what, (int)(pos));
   }
   pos = any_duplicated(nn, FALSE);
-  
+
   if (pos > 0) {
     UNPROTECT(1);
-    Rf_errorcall(R_NilValue, "Must have unique %s, but element %i is duplicated", what, pos);
+    Rf_errorcall(R_NilValue, "Must have unique %s, but element %i is duplicated", what, (int)(pos));
   }
-  
+
   if (isNull(nn)) {
     UNPROTECT(1);
     Rf_errorcall(R_NilValue, "Must have %s", what);
   }
   pos = any_duplicated(nn, FALSE);
   if (pos > 0){
     UNPROTECT(1);
-    Rf_errorcall(R_NilValue, "Must have unique %s, but element %i is duplicated", what, pos);
+    Rf_errorcall(R_NilValue, "Must have unique %s, but element %i is duplicated", what, (int)(pos));
   }
   pos = check_strict_names(nn);
   if (pos > 0){
     UNPROTECT(1);
-    Rf_errorcall(R_NilValue, "Must have %s according to R's variable naming conventions, but element %i does not comply", what, pos);
+    Rf_errorcall(R_NilValue, "Must have %s according to R's variable naming conventions, but element %i does not comply", what, (int)(pos));
   }
   UNPROTECT(1);
 }